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The Mystery of Evolution: 8. Common Descent-The Tree of Life or a Bush? An Orchard?

It turns out that professor Larry Moran of the University of Toronto agrees with Craig Venter. Thanks to Allan Miller, I discovered a blog on a similar theme at sandawalk link here

This is what professor Moran says about the video (his video is 42 min long):

” Everything that Ventor says is correct. He didn’t need to quibble about the universality of the genetic code but it’s true that there are variants.”

“I’m pretty sure that Dawkins doesn’t agree (in reference to video) with those who question whether there’s a tree of life. One of the most profound implications of the net of life is that it’s consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species. In other words, there may not be a single LUCA (Last Universal Common Ancestor). Dawkins does not like that. It’s not what he says on the lecture circuit.” (my emphasis)

There is probably no one in the world of biology today as respected as Craig Venter.

Why?

Well, his achievements are indeed great including being involved with sequencing the human genome and assembled the first team to transfect a cell with a synthetic chromosome, which some even went as far as calling the creation of artificial life…

Now apparently, he is involved in the anti-aging research…no surprise here…he is 70 and would like reach immortality like the jellyfish…Who can blame him…He is an atheist…

However, his also known for what some would call radical statements such as denying the common descent which is the very foundation of evolutionary theory…

“Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. Common ancestry between organisms of different species apparently arises during speciation, in which new species are established from a single ancestral population. Organisms which share a more recent common ancestor are apparently closely related.” –Wiki

The apparent common descent of all organisms on earth doesn’t agree with Craig Venter’s research…

Here is what he says on the theme:

While some may object that this is an old and recycled subject, I would argue that to claim that, one would have to present the evidence that Venter’s claims have been refuted since…

However, in view of my recent OPs The Mystery of Evolution # 6 especially, it doesn’t look like the issue of common ancestry has been resolved at all…The genes are still not accounted for and the proposed mechanism for the endosymbiosis seems sketchy… if not miraculous…

If anything, the supposed common ancestry got more complicated on the much deeper and deeper level in the history of life and no wonder that Venter claims that:

Venter: “…I’m not so sanguine as some of my colleagues here,” he said, “that there’s only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you [Venter said, turning to physicist Paul Davies, on his right] the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.”

What does he mean by this? Is there more then one form life on earth?

Davies “Well, I’ve got the same genetic code, “We’ll have a common ancestor.”

Venter: “You don’t have the same genetic code,” replied Venter. “In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”

Davies: “But you’re not saying it [i.e., Mycoplasma] belongs to a different tree of life from me, are you?”

Venter: There Isn’t a Tree of Life

“The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”

What Venter was talking about” is as good, if not better today, and it will look even better in the not that distant future…I can assure you of that… 🙂

75 Replies to “The Mystery of Evolution: 8. Common Descent-The Tree of Life or a Bush? An Orchard?”

I note also that J-Mac has discovered a rather touching fondness for the work of Larry Moran, since he sides with Venter in the opening post at Sandwalk, prompting J-Mac to line him up in his own. Again, to save composing posts to order, here is the estimable Miller responding to Witton, who had tried to over-egg the significance of variant codes:

I’m suggesting – no, saying – that you are making something out of nothing. Venter did not say anything incorrect – and neither did Dawkins. This was a comparatively informal conversation. The title “Venter makes a fool of Dawkins” is just bollocks.

Person A: “America and England use the same language”
Person B: “They do not share the same language – there are many differences”
Person A: “OK, I see what you mean – but they are clearly related … aren’t they?”

That is the nature of Venter’s “Mycoplasma” distinction. UGA codes for tryptophan instead of STOP. That’s it. 63 out of 64 codons shared. I think you (and, for different reasons, Prof. Moran) are just indulging a little gratuitous Dawkins-bashing. I’m pretty sure he understands both HGT and the nature of ‘different codes’.

Larry Moran seems to be a fan of the ‘progenote’ ideas of Carl Woese. I’m not. But I don’t know why he doesn’t emphasise the above, instead giving a gift to the more clueless in his audience, as we can see above.

So now I have said ‘Venter is wrong’ and ‘he didn’t say anything incorrect’. Knowing the audience as I do, let me be clear: he is wrong in concluding that the evidence points against a single origin of life.

The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.” (Penny and Hendy 1986, p. 414)

I wonder if any equivalent brief exchange has been subject to as much scrutiny as this one between Dawkins and Venter!

I saw one version of this vid. Dawkins makes the reasonable point “the DNA code of all creatures that have ever been looked at is all but identical. Surely that means that they are all related … doesn’t it?”. Venter laughs, the screen goes black and up pops the commentary:

“Craig Venter never responded (but laughs at Dawkins). Ever since this video came out, Darwinian fundamentalists have gone loco doing damage control – even going as far as lying about Venter! These evolutionary wackos just can’t bring it to themselves to accept facts even when it’s right in front of them”.

Abstract
The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of ‘Lokiarchaeota’, a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic ‘starter-kit’ to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

ABSTRACT
The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.
(…)
6. CONCLUSION
Four groups of recent observations increase the plausibility of the symbiogenetic scenario for the origin of eukaryotes. The first line of evidence comes from the reconstructions of archaeal genome evolution which imply complex ancestral forms, with the subsequent evolution in most lineages dominated by gene loss. The related and perhaps most important clues come from the observations on the archaeal eukaryome that is scattered among diverse extant archaea. The putative complex archaeal ancestor of eukaryotes could have encoded most if not all components of the eukaryome within the same genome, possibly endowing this ancestral archaeon with certain eukaryote-like functionalities such as the ability to efficiently engulf other cells (a primitive version of phagocytosis). The third line of evidence consists of the increasingly confident demonstrations of the origin of the core eukaryotic genes from within the archaea, or more specifically, from a deeply branching group within the TACK superphylum. Given that all known extant members of this superphylum are typical archaea and not archezoa, these findings appear to favour an archaeal host for the proto-mitochondrial endosymbiont. Finally, the indications that massive acquisition of bacterial genes most probably triggered the emergence of the major groups of archaea put the origin of eukaryotes into a more general evolutionary context. These discoveries make the origin of eukaryotes appear less dramatically different from the origin of other groups of organisms than is generally perceived. Horizontal transfer of numerous genes appeared to have been central in each case. The key difference is that in eukaryotes the source of the foreign genes, i.e. the endosymbiont, survived as an organelle, precipitating the radical restructuring of the cell. Given the likely origin of eukaryotes from within the archaeal diversity and the observations on the dispersed eukaryome, there seems to be high promise of new evolutionary insights coming from metagenomics and single-cell genomics. The discovery of archaeal descendants of the elusive host of the mitochondrial endosymbiont cannot be ruled out.

Allan Miller: Larry Moran seems to be a fan of the ‘progenote’ ideas of Carl Woese. I’m not. But I don’t know why he doesn’t emphasise the above, instead giving a gift to the more clueless in his audience, as we can see above.

True, although Moran really did side with Venter and against Dawkins on this. I think he misinterpreted Dawkins’s point, which wasn’t about the ‘greater tree’ at all, but about Venter’s peculiar Mycoplasma contentions.

The old tree of life based on ribosomal RNA has a single common ancestor. The modern net of life, based on a large number of genes, does not. Therefore it is not scientifically correct to say that all modern species descend from a single common ancestor. You can say that, based on currently available scientific evidence, there was probably a single origin of life but that’s not the same thing.

Allan Miller:

I appreciate the point, but when you chide Dawkins for doggedly clinging to some outmoded paradigm, you present no sound reason he should do otherwise. Theobald and clear commonality in most codons point to a single organism, and AFAIK no evidence points the other way. The HGT that muddies multi-gene trees is still in protein-coding organisms, and they still have mostly invariant codons, and ribosomes, and tRNA and aaRS, suggesting all the shuffling has happened since those were fixed. It’s possible (though unlikely) that the genetic code itself was cobbled by HGT of codon assignments from multiple organisms, but even so, what were they most likely descended from – common, or different, ancestors?

What went on before that ‘bottleneck’ organism from which we appear to have inherited a DNA-RNA-protein system already pretty well fixed is up for grabs, but there does appear to have been a genuine bottleneck***, on the evidence. According to Theobald, the scrambled phylogenies still resolve on a single ancestor. And that’s as far back as we can get.

There is nothing in principle forbidding multiple origins – except the need for convergence of some kind to permit their merger. So I can accept it as a possibility, and I’m sure Dawkins would too. There’s just no evidence for it.

Craig doesn’t make anything clear. None of the terms are defined. What does he mean by another “form” of life. He points out metabolic differences between different domains. Does that make them another “form” of life? Surely he doesn’t mean they’re no longer cellular life? Doesn’t the idea of a domain merely constitute another branching on a tree or a bush? Doesn’t he in fact use the term “deep branching” himself? What publications are there on this by Venter et al?
I found this: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees“Abstract:
Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.

Methodology/Principal Findings:
We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.

Conclusions/Significance:
Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.”

It seems to me there’s nothing in here about the genetic code not implying common descent, and the short exchange of words between Dawkins and Venter was actually more confusing than informative. In fact I think they talked past each other. Dawkins was concerned with whether there is universal common descent (and whether the genetic code implies this), while Craig was concerned with whether the root of the tree of life is a bush rather than a single stem. It seems neither of them got what the other one was saying.

Here’s what amuses me, J-Mac: in your OP Mystery#6, which is all about endosymbiosis, you quote-mine statements by W. Ford Doolittle on the fact that HGT was prevalent in early evolution, such that the base of the tree of life is rather network-like.
You are impressed with Doolittle, because you think he is agreeing with you. (He isn’t, but that’s not important right now. 😉 )
But, irony of ironies, Doolittle is one of the original researchers who showed that chloroplasts were the result of an endosymbiotic event!
Hence my question:

Does this “impressed” feeling also extend to Dr. Doolittle’s views on endosymbiosis and on junk DNA, I wonder?

Did all this HGT happen before or after the emergence of spliceosomal introns in Eukaryotes.

I would presume the mainstream theory agues for before, right?

Probably after, actually. IIRC there are introns in Archaea – though they may not be ancient.

I’m surprised no-one has mentioned the different genetic codes in mitochondria, plastids and nuclei yet. “It’s impossible! They’re a different life form, right? You can’t put the genes from one in the other!”. Chortle. 🙂

I’m surprised no-one has mentioned the different genetic codes in mitochondria, plastids and nuclei yet. “It’s impossible! They’re a different life form, right? You can’t put the genes from one in the other!”. Chortle.

No-one? Oh, come on! This could not be more germane to this OP and #6 if it came with a Certificate of Germaneness from the Germane Institute.

There are more differences between our mitochondrial and our nuclear codes (4) than there are between Mycoplasma and our nuclei (1). One of the differences between our mitochondrial and nuclear codes is actually the same as the one difference between Mycoplasma and our nuclei: UGA is Tryptophan instead of STOP. So, Mycoplasma is closer to both our nuclear codes (63/64) and our mitochondrial codes (61/64) than either is to the other (60/64). Interestingly, UGA is sometimes not STOP even in nuclei, but selenocysteine. And, STOPs are often position-dependent, being ‘read through’ if they are some distance away from the poly-A tail.

So mitochondria have their own ribosomes and their own tRNA? What about chloroplasts?

Yes. Like mitochondria, they contain much (though not all) of the protein synthesis machinery plus numerous organelle-specific proteins – though again, by no means all.

I wrote two lengthy comments in the ‘Prediction Tested’ thread about gene migration, including the question of what remains, and why. The second isn’t relevant to that question, but shame to let it go to waste!